Add some way to 'link' and/or describe the cohort that is being diagnosed - Githubissues

OHDSI / CohortDiagnostics

An R package for performing various cohort diagnostics.

https://ohdsi.github.io/CohortDiagnostics

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Add some way to 'link' and/or describe the cohort that is being diagnosed #82

Closed pbr6cornell closed 4 years ago

pbr6cornell commented 4 years ago

Currently, we only have a cohort name, but there is no way to map back from the cohort name to the correesponding cohort being executed. If that cohort was generated in ATLAS, would be useful to link out, and/or have print friendly description.

gowthamrao commented 4 years ago

https://github.com/OHDSI/CohortDiagnostics/issues/90

gowthamrao commented 4 years ago

https://github.com/OHDSI/CohortDiagnostics/issues/80

gowthamrao commented 4 years ago

Implementation in Charydbis

Implemented in Charydbis through https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis/pull/60

Similarly in Cohort Diagnostics -

add to 'Cohort Counts' submenu
in data table, make each row in dt for column DT a hyperlink
cohort count table uses cohort table in premerged file. This table also has atlasId field
use default baseUrl = 'https://atlas.ohdsi.org/#/'
for hyperlink use paste0(baseUrl, 'cohortdefinitions/', atlasId)

gowthamrao commented 4 years ago

Added interim solution. Using cohortId as presumed AtlasId. Base URL defaults to ohdsi Atlas, but maybe overwritten in shiny app

gowthamrao commented 4 years ago

https://github.com/OHDSI/CohortDiagnostics/issues/144

gowthamrao commented 4 years ago

Current implementation of link out

use cohortId
use default url to append the cohort id here https://github.com/OHDSI/CohortDiagnostics/blob/61e58c8abf5cc8ec91dc2b6b110a1ef8bf90e228/inst/shiny/DiagnosticsExplorer/ui.R#L191
add ability for user to modify it in shiny app using shiny's reactive function here https://github.com/OHDSI/CohortDiagnostics/blob/master/inst/shiny/DiagnosticsExplorer/server.R#L97-L98

Future version

assumption: atlas cohort definitions are stable and dont change over time, i.e. link outs to atlas are stable and persistent
we can allow end-user to provide atlasUrl as a parameter during the creation of premerged file. Then we can generate the link out to these cohort definitions using the atlasUrl in premerged data.

gowthamrao commented 4 years ago

A proposed version - that we may not implement

we cohort json expression in cohort.csv
post expression into any available webapi/atlas of user choice to instantiate (on fly) the atlas cohort definition page from the cohort json expression (done using ROhdsiWebApi). When user comes back to shiny app - delete the instantiated cohort